Missions

This postdoctoral contract is based on the Emergence HisModSim project obtained by Natacha Gillet at the Laboratoire de Chimie of the ENS de Lyon. It focuses on the impact of post-translational modifications or histone variant modifications in the nucleosome, the primary unit of chromatin, using classical all-atom molecular dynamics simulations. The nucleosome is composed of a double-stranded DNA fragment wrapped around a protein core consisting of eight histones. These proteins are highly conserved in living organisms but can undergo post-translational modifications that can tune gene activation, replication, DNA repair, etc. In addition, histone variants can be exchanged and associated with biological processes such as the circadian rhythm. The aim of the project is to understand at a molecular level the impact of these modifications on the structure and dynamics of the nucleosome, more specifically in the context of oxidative DNA damage and circadian rhythm regulation, in collaboration with IGFL.

Activités

The post-doctoral researcher will:
- run a large data set of classical molecular dynamics simulations of modified nucleosomes
- analyze the large data set obtained using various analysis tools, from visualization to automation using machine learning tools
- perform QM/MM calculations on specific aspects
- keep up to date with the literature on both methodological and molecular biology aspects
- communicate the results at conferences and through scientific articles

Compétences

Candidates must have experience in computational chemistry. Expertise in classical molecular dynamics simulations, preferably on biological systems, is expected. Programming and/or machine learning skills will be appreciated.

Contexte de travail

The research will be carried out within the Theoretical Chemistry and Molecular Thermodynamics axis of the Laboratoire de Chimie ENS Lyon. Our group covers several topics in theoretical and computational chemistry (static and dynamic photochemistry, heterogeneous catalysis, modeling of interfaces and ionic liquids). It benefits from access to the CBPSMN mesocenter, with a large amount CPUs and GPUs facilities. In addition, computing time on national centers (GENCI) is allocated for this project.

Contraintes et risques

Computational work only